That's what we thought in EoE, but you see how that
EVA-01 didn't killed anyone when she emerged from NERV in EoE, the only killing was under Shinji's crazed orders.
It's possible that EVA-01 will again tang humanity in Shin, but I don't think that it'll kill people before that, especially not the people of the Wunder, which is presented as mankind's greatest hope and its crew as the next generation that will inherit Earth and the symbol of humanity struggling to carve her own path.
Having them being wiped out by Unit 01 would be like in NGE, as if Yui appeared, spat on WILLE and told them "nope, all of your struggles were meaningless, everything was already predestined by virtue of one woman that installed herself in this purple abomination 24 years ago, and the resolution of the conflict will be exclusively in the hands of the people I
have chosen and there's nothing you can do to stop me, but thanks for entertaining us!"
And frankly that would be lame. NGE had a foreboding sense of impending apocalypse, something that deep down tell us that it won't end well and that in the end the apocalypse will
happen since there are too many forces at works to bring it (albeit with different results in mind) and too little trying to oppose it, but in NTE it's very different: for once the good guys managed to unite into a coherent and strong force able to fight the ancestral conspiracy and be a genuine threat to their plan (or at least something they can't overlook as insignificant, as poor Misato was in EoE), the fabled apocalypse was even averted twice
! (trice if there really was another Third Impact involving the 12th Angel) so having it subverted by making their struggle meaningless again and their fate tied to the whims of a select few, as if everything was fated since the beginning, well frankly that would sucks for me.